Team:Michigan/Modeling

From 2013.igem.org

(Difference between revisions)
(Switch modeling)
(Mass action modeling)
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===Mass action modeling===
===Mass action modeling===
-
• what is mass action
+
Definition
-
pros of mass action modeling, i.e. why we used it
+
differential equations
 +
 
 +
• each equation is a sum of rates
 +
 
 +
• each rate is proportional to each of its reactants
 +
 
 +
[[File:mass action.jpg]]
 +
 
 +
Benefits of mass action modeling, i.e. why we used it
• form of mass action models/solvability doc
• form of mass action models/solvability doc

Revision as of 00:31, 28 September 2013

Xayona Website Template

Best model.jpg

Contents

Introduction

Switch modeling

• produce both states of switch

• use model to optimize switch

Mass action modeling

Definition

• differential equations

• each equation is a sum of rates

• each rate is proportional to each of its reactants

File:Mass action.jpg

Benefits of mass action modeling, i.e. why we used it

• form of mass action models/solvability doc

Analytical modeling

• benefits

   • naturally standardized
   
   • given parameters, it precisely predicts behavior
   • accurately predicts the data needed to determine parameters
   • allows avoidance of numerical errors like rounding

• ERSESCO

   • equation
   • reduction
   • solution
   • equilibration
   • stabilization
   • calibration
   • optimization

SimBiology

• numerical approximation

• diagram / schematic

Model of Recombinase Expression

Model of the Switch

Model of Inducible Hbif

Expression Model

ExpressionModelFigure.png

Equation:

ExpressionModel1.png

Reduction: None

Solution:

ExpressionModel2.png

Equilibration:

ExpressionModel3.png

Stabilization:

ExpressionModel3-1.png

Calibration:

ExpressionModel4.png
ExpressionModel5.png

Optimization:

ExpressionModel6.png

SimBiology:

Expression.jpg

Expression Model Derivation

Switch Model

SwitchModelFigure.png

Equation:

SwitchModel1.png
SwitchModel2.png

Reduction:

SwitchModel3.png

Solution:

SwitchModel3-1.png

Equilibration:

SwitchModel4-1.png

Stabilization:

SwitchModel4-2.png

Calibration:

SwitchModel5-1.png
SwitchModel5-2.png

Optimization:

SwitchModel6.png

SimBiology:

Switch.jpg

Switch Model Derivation

Inducible Hbif Model

InducibleHbifModelFigure.png

Equation:

InducibleHbifModel1.png
InducibleHbifModel2.png

Reduction:

InducibleHbifModel3.png

Solution:

InducibleHbifModel4.png

Equilibration:

InducibleHbifModel5.png

Stabilization:

InducibleHbifModel5-2.png

Calibration:

InducibleHbifModel6-1.png
InducibleHbifModel6-2.png
InducibleHbifModel6-3.png

Optimization of Hbif:

InducibleHbifModel7-1.png

Optimization of ON:

InducibleHbifModel7-2.png

SimBiology:

InducedHbif.jpg

Inducible Hbif Model Derivation

Future Directions

Data!

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